# US 2014/0156236 A1 · Modeling multiple interactions between multiple loci

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- Number: US 2014/0156236 A1
- Document ID: US20140156236A1
- Status: Published application
- Kind: A1
- Application number: 14/030,787
- Filed: 2013-09-18
- Published: 2014-06-05
- Earliest claimed: 2012-12-05
- Assignees: International Business Machines Corporation
- Applicants: International Business Machines Corporation
- Inventors: David C. HAWS; Dan HE; Laxmi P. PARIDA
- Web page: https://patentgrep.com/patent/US20140156236A1

## CPC

- G16B 5/00: ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
- G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## Abstract

Various embodiments generate a quantitative model of genetic effect. In one embodiment, a processor receives a set of loci of an entity. Each locus is associated with a contribution value to a given physical trait. A first set of interacting loci associated with a first interaction and at least a second set of interacting loci associated with at least a second interaction are identified. The first interaction type is associated with a first interaction model. The at least the second interaction is associated at least a second interaction model. A model of a quantitative value of the entity is generated based on at least the contribution value associated with each locus in the set of loci, a contribution value of the first interaction as defined by the first interaction model, and a contribution value of the second interaction as defined by the at least the second interaction model.

## Claims

### Claim 1

An information processing system for generating a quantitative model of genetic effect, the information processing system comprising:
a memory;
a processor communicatively coupled to the memory; and
an interaction model generator communicatively coupled to the memory and the processor, wherein the interaction model generator is configured to perform a method comprising:
receiving a set of loci of an entity, wherein each locus in the set of loci is associated with a contribution value to a given physical trait;
identifying, from the set of loci, a first set of interacting loci associated with a first interaction and at least a second set of interacting loci associated with at least a second interaction, wherein the first interaction is associated with a first interaction model, and wherein the at least the second interaction is associated at least a second interaction model;
generating a model of a quantitative value of the entity based on at least
the contribution value associated with each locus in the set of loci,
a contribution value of the first interaction as defined by the first interaction model, and
a contribution value of the at least the second interaction as defined by the at least the second interaction model.

### Claim 2 (depends on 1)

The information processing system of claim 1, wherein the model of the quantitative value is defined as a
V
j
:=
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N
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i
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ij
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i
1
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=
A
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f
i
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x
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x
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where Vj is the model of the quantitative value, j is an entity, Variable j is the individual, i is a locus, N is a real number, βi is an impact scaling factor for locus i, xij is a contribution encoding of locus i, k is an integer identifying a number of interacting loci, I is a set of interacting loci, f is an interaction model, and iA is a set of loci A using the interaction model f.

### Claim 3 (depends on 1)

The information processing system of claim 1, wherein the method further comprises:
identifying at least one of the first set of interacting loci and the at least the second set of interacting loci are from real data.

### Claim 4 (depends on 1)

The information processing system of claim 1, wherein the first set of interacting loci and the at least the second set of interacting loci are identified based on input received from a user.

### Claim 5 (depends on 1)

The information processing system of claim 1, wherein the method further comprises:
determining that at least one of the first interaction model and the at least the second interaction model are associated with the first interaction and the at least the second interaction, respectively, based on real data.

### Claim 6 (depends on 1)

The information processing system of claim 1, wherein the method further comprises:
receiving, from a user, at least one of
an association of the first interaction model with the first interaction, and
an association of the at least the second interaction model with the at least the second interaction.

### Claim 7

A computer program product for generating a quantitative model of genetic effect, the computer program product comprising:
a storage medium readable by a processing circuit and storing instructions for execution by the processing circuit for performing a method comprising:
receiving a set of loci of an entity, wherein each locus in the set of loci is associated with a contribution value to a given physical trait;
identifying, from the set of loci, a first set of interacting loci associated with a first interaction and at least a second set of interacting loci associated with at least a second interaction, wherein the first interaction is associated with a first interaction model, and wherein the at least the second interaction is associated at least a second interaction model;
generating a model of a quantitative value of the entity based on at least
the contribution value associated with each locus in the set of loci,
a contribution value of the first interaction as defined by the first interaction model, and
a contribution value of the at least the second interaction as defined by the at least the second interaction model.

### Claim 8 (depends on 7)

The computer program product of claim 7, wherein the model of the quantitative value is defined as a
V
j
:=
∑
i
N

β
i

x
ij
+
∑
{
i
1
,
…

,
i
k
}
=
A
∈
I

f
i
A

(
x
i
1

j
,
…

,
x
i
k

j
)
where Vj is the model of the quantitative value, j is an entity, Variable j is the individual, i is a locus, N is a real number, βi is an impact scaling factor for locus i, xij is a contribution encoding of locus i, k is an integer identifying a number of interacting loci, I is a set of interacting loci, f is an interaction model, and iA is a set of loci A using the interaction model f.

### Claim 9 (depends on 7)

The computer program product of claim 7, wherein the method further comprises:
identifying at least one of the first set of interacting loci and the at least the second set of interacting loci are from real data.

### Claim 10 (depends on 7)

The computer program product of claim 7, wherein the first set of interacting loci and the at least the second set of interacting loci are identified based on input received from a user.

### Claim 11 (depends on 7)

The computer program product of claim 7, wherein the method further comprises:
determining that at least one of the first interaction model and the at least the second interaction model are associated with the first interaction and the at least the second interaction, respectively, based on real data.

### Claim 12 (depends on 7)

The computer program product of claim 7, wherein the method further comprises:
receiving, from a user, at least one of
an association of the first interaction model with the first interaction, and
an association of the at least the second interaction model with the at least the second interaction.